Anti-cancer effect and mechanism of cell death were investigated in a battery of five thalidomide analogs containing one sulfur atom 2 or two sulfur atoms 3–6 and were compared with thalidomide 1 activity. The cytotoxic effect of thalidomide analogs 2–6 against Hep-G2, 1301, and HCT-116 cells was estimated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Apoptosis and necrosis cell percentage was stained by ethidium bromide and acridine orange, DNA fragmentation, inhibition of histone deacetylase (HDAC), and total caspases were assayed by universal procedures and kits. We report here for the anti-cancer activity of thalidomide dithiocarbamate analog 3 and thalidomide dithioate analog 5 against Hep-G2 and HCT-116 cells, which was more cytotoxic than thalidomide itself, and that the cytotoxicity was associated with DNA fragmentation and was due to apoptosis and not necrosis. Moreover, we suggest that the cell death pathway is evoked by thalidomide dithiocarbamate analog 3 and thalidomide dithioate analog 5 in human hepatocellular carcinoma cells through multiple consequences that trigger apoptotic cell death; involving the enhancement of DNA fragmentation, the activation of caspases, and the induction of histone acetylation. In conclusion, thalidomide dithiocarbamate analog 3 and thalidomide dithioate analog 5 are promising anti-cancer agents more than thalidomide.